Communicating the promise, risks, and ethics of large-scale, open space microbiome and metagenome research

The public commonly associates microorganisms with pathogens. This suspicion of microorganisms is understandable, as historically microorganisms have killed more humans than any other agent while remaining largely unknown until the late seventeenth century with the works of van Leeuwenhoek and Kircher. Despite our improved understanding regarding microorganisms, the general public are apt to think of diseases rather than of the majority of harmless or beneficial species that inhabit our bodies and the built and natural environment. As long as microbiome research was confined to labs, the public's exposure to microbiology was limited. The recent launch of global microbiome surveys, such as the Earth Microbiome Project and MetaSUB (Metagenomics and Metadesign of Subways and Urban Biomes) project, has raised ethical, financial, feasibility, and sustainability concerns as to the public's level of understanding and potential reaction to the findings, which, done improperly, risk negative implications for ongoing and future investigations, but done correctly, can facilitate a new vision of "smart cities." To facilitate improved future research, we describe here the major concerns that our discussions with ethics committees, community leaders, and government officials have raised, and we expound on how to address them. We further discuss ethical considerations of microbiome surveys and provide practical recommendations for public engagement

The effect of tidal flow directionality on tidal turbine performance characteristics

With many Tidal Energy Conversion (TEC) devices at full scale prototype stage there are two distinct design groups for Horizontal Axis Tidal Turbines (HATTs). Devices with a yaw mechanism allowing the turbine to always face into the flow, and devices with blades that can rotate through 180° to harness a strongly bi-directional flow. As marine turbine technology verges on the realm of economic viability this paper reveals the performance of Cardiff University's concept tidal turbine with its support structure either upstream or downstream and with various proximities between the rotating plane of the turbine and its support stanchion. Through the use of validated Computational Fluid Dynamics (CFD) modelling this work shows the optimal proximity between rotor plane and stanchion as well as establishing, in the given context, the use of a yaw mechanism to be superior to a bi-directional system from a performance perspective

Altered m6A Modification of Specific Cellular Transcripts Affects Flaviviridae Infection

The RNA modification N6-methyladenosine (m6A) modulates mRNA fate and thus affects many biological processes. We analyzed m6A across the transcriptome following infection by dengue virus (DENV), Zika virus (ZIKV), West Nile virus (WNV), and hepatitis C virus (HCV). We found that infection by these viruses in the Flaviviridae family alters m6A modification of specific cellular transcripts, including RIOK3 and CIRBP. During viral infection, the addition of m6A to RIOK3 promotes its translation, while loss of m6A in CIRBP promotes alternative splicing. Importantly, viral activation of innate immune sensing or the endoplasmic reticulum (ER) stress response contributes to the changes in m6A in RIOK3 or CIRBP, respectively. Further, several transcripts with infection-altered m6A profiles, including RIOK3 and CIRBP, encode proteins that influence DENV, ZIKV, and HCV infection. Overall, this work reveals that cellular signaling pathways activated during viral infection lead to alterations in m6A modification of host mRNAs to regulate infection. Here, Gokhale, McIntyre et al. identify m6A changes in cellular mRNAs following Flaviviridae infection and demonstrate that infection-activated pathways contribute to these changes. They show that altered m6A modification in RIOK3 and CIRBP mRNAs influence their translation and splicing, respectively, and that RIOK3, CIRBP, and other m6A-altered factors regulate infection

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

DNA methylation is a chemical modification of cytosine bases that is pivotal for gene regulation, cellular specification and cancer development. Here, we describe an R package, methylKit, that rapidly analyzes genome-wide cytosine epigenetic profiles from high-throughput methylation and hydroxymethylation sequencing experiments. methylKit includes functions for clustering, sample quality visualization, differential methylation analysis and annotation features, thus automating and simplifying many of the steps for discerning statistically significant bases or regions of DNA methylation. Finally, we demonstrate methylKit on breast cancer data, in which we find statistically significant regions of differential methylation and stratify tumor subtypes. methylKit is available at http://code.google.com/p/methylkit

Forensic applications of microbiomics: a review

The rise of microbiomics and metagenomics has been driven by advances in genomic sequencing technology, improved microbial sampling methods, and fast-evolving approaches in bioinformatics. Humans are a host to diverse microbial communities in and on their bodies, which continuously interact with and alter the surrounding environments. Since information relating to these interactions can be extracted by analyzing human and environmental microbial profiles, they have the potential to be relevant to forensics. In this review, we analyzed over 100 papers describing forensic microbiome applications with emphasis on geolocation, personal identification, trace evidence, manner and cause of death, and inference of the postmortem interval (PMI). We found that although the field is in its infancy, utilizing microbiome and metagenome signatures has the potential to enhance the forensic toolkit. However, many of the studies suffer from limited sample sizes and model accuracies, and unrealistic environmental settings, leaving the full potential of microbiomics to forensics unexplored. It is unlikely that the information that can currently be elucidated from microbiomics can be used by law enforcement. Nonetheless, the research to overcome these challenges is ongoing, and it is foreseeable that microbiome-based evidence could contribute to forensic investigations in the future

The impact of cross-kingdom molecular forensics on genetic privacy

Recent advances in metagenomic technology and computational prediction may inadvertently weaken an individual’s reasonable expectation of privacy. Through cross-kingdom genetic and metagenomic forensics, we can already predict at least a dozen human phenotypes with varying degrees of accuracy. There is also growing potential to detect a “molecular echo” of an individual’s microbiome from cells deposited on public surfaces. At present, host genetic data from somatic or germ cells provide more reliable information than microbiome samples. However, the emerging ability to infer personal details from different microscopic biological materials left behind on surfaces requires in-depth ethical and legal scrutiny. There is potential to identify and track individuals, along with new, surreptitious means of genetic discrimination. This commentary underscores the need to update legal and policy frameworks for genetic privacy with additional considerations for the information that could be acquired from microbiome-derived data. The article also aims to stimulate ubiquitous discourse to ensure the protection of genetic rights and liberties in the post-genomic era

Kinetic energy extraction of a tidal stream turbine and its sensitivity to structural stiffness attenuation

© 2015 The Authors. The hydrodynamic forces imparted on a tidal turbine rotor, whilst causing it to rotate and hence generate power, will also cause the blades to deform. This deformation will affect the turbine's performance if not included in the early design phase and could lead to a decrease in power output and a reduction in operational life. Conversely, designing blades to allow them to deform slightly may reduce localised stress and therefore prolong the life of the blades and allow the blades to deform in to their optimum operational state. The aim of this paper is to better understand the kinetic energy extraction by varying the material modulus of a turbine blade. Shaft torque/power, blade tip displacement, and axial thrust results are presented for 2, 3 and 4 bladed rotor configurations at peak power extraction. For the rotor design studied the FSI model data show that there is a low sensitivity to blade deformation for the 2, 3 and 4 bladed rotors. However, the results reveal that the 3 bladed rotor displayed maximum hydrodynamic performance as a rigid structure which then decreased as the blade deformed. The 2 and 4 bladed rotor configurations elucidated a slight increase in hydrodynamic performance with deflection

Genomic DNA transposition induced by human PGBD5

Transposons are mobile genetic elements that are found in nearly all organisms, including humans. Mobilization of DNA transposons by transposase enzymes can cause genomic rearrangements, but our knowledge of human genes derived from transposases is limited. In this study, we find that the protein encoded by human PGBD5, the most evolutionarily conserved transposable element-derived gene in vertebrates, can induce stereotypical cut-and-paste DNA transposition in human cells. Genomic integration activity of PGBD5 requires distinct aspartic acid residues in its transposase domain, and specific DNA sequences containing inverted terminal repeats with similarity to piggyBac transposons. DNA transposition catalyzed by PGBD5 in human cells occurs genome-wide, with precise transposon excision and preference for insertion at TTAA sites. The apparent conservation of DNA transposition activity by PGBD5 suggests that genomic remodeling contributes to its biological function

A Performance Analysis Framework for WiFi/WiMAX Heterogeneous Metropolitan Networks Based on Cross-Layer Design

The communication between network nodes within different protocol domains is often regarded simply as a black box with unknown configuration conditions in the path. We address network heterogeneity using a white box approach and focus on its interconnection processes. To achieve this purpose, a Performance Analysis Framework (PAF) is proposed which is composed of the formalization of the latter using process algebra (PA) and the corresponding teletraffic performance models. In this contribution, we target the IEEE 802.16 and IEEE 802.11 protocols. For the teletraffic models, we extend previous models for such scenario with the inclusion of the following protocol operational parameters (metrics): bit error rate (BER), packet error ratio (PER), and packet length (pl). From the framework teletraffic models, the optimal packet length (OPL), end to end throughput, delay, and packet loss are obtained. The PAF outperforms previous modeling solutions in terms of delay and throughput relative to NS3 simulation results. </jats:p